Home » Intelligent Design » Where Are the Neutral Genomes with these Mutations?

Where Are the Neutral Genomes with these Mutations?

As readers of UD know, Elizabeth Liddle is convinced that in any population there are neutral versions of the genome that have every needed variation an organism must have. Change the environment, and, lo and behold, the organism changes.

But what has happened here? Let’s quote the article:

H5N1 evolved in poultry in east Asia and has spread across Eurasia since 2004. In that time 565 people are known to have caught it; 331 died. No strain that spreads readily among mammals has emerged in that time, despite millions of infected birds, and infections in people, cats and pigs. Efforts to create such a virus in the lab have failed, and some virologists think H5N1 simply cannot do it.

Where are the neutral mutations?

But, don’t be disheartened. Scientists were finally able to make something happen:

The work by Fouchier’s team suggests otherwise. They first gave H5N1 three mutations known to adapt bird flu to mammals. This version of the virus killed ferrets, which react to flu viruses in a similar way to humans. The virus did not transmit between them, though.

But they weren’t quite yet there:

Then the researchers gave the virus from the sick ferrets to more ferrets – a standard technique for making pathogens adapt to an animal. They repeated this 10 times, using stringent containment. The tenth round of ferrets shed an H5N1 strain that spread to ferrets in separate cages – and killed them.

Aw….the wonders of “artificial selection”!! Darwin tells us that nature is scrutinizing everything, all the time, and that “natural selection” is, thus, so much more powerful than “artificial selection”. But wait a sec. . . . NS can’t think. It’s not goal oriented. But intelligent agents are. And, so, they ultimately found a solution to something nature was unable to; thus, disproving Darwin’s claim that NS is more powerful than AS. Darwin is once again shown to be wrong—as he is in just about every case. But, no matter: Darwinists are “true believers”!!

Oh, BTW, someone appears to have been proven correct. Let’s take a closer look:

The process yielded viruses with many new mutations, but two were in all of them. Those plus the three added deliberately “suggest that as few as five are required to make the virus airborne”, says Fouchier. He will now test H5N1 made with only those five.

Let’s see: three mutations are manufactured by humans, and two mutations—found in all the developed strains—by nature. Now that sounds familiar, doesn’t it? Yes, of course, the very same conclusion that Michael Behe came to in his Edge of Evolution!

So: Behe is right; and Darwin is wrong. What are we to expect from the Darwinist “true believers”? Denial and derision. All hail the ‘scientific method’ and its best friend, ‘naturalism’.

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36 Responses to Where Are the Neutral Genomes with these Mutations?

  1. “in any population there are neutral versions of the genome that have every needed variation an organism must have. Change the environment, and, lo and behold, the organism changes.”

    Or the variation the “organism must have” isn’t present and the organism goes extinct.

    Considering evolutionary biologists think much, much more life is extinct than extant, your criticism seems misplaced.

    Knowing what flu is capable, and likely to evolve into is helpful in predicting and thwarting it.

    In Elizabeth Liddle’s defense, I don’t think she would ever say such a thing. If I were you, I’d either link directly to her statement, or retract it promptly, with apologies.

  2. By the way, since mammals are much more seldom infected, and as yet, dead-end hosts for this flu, there is really little variation that has been tested and selected for transmission in them. So those simultaneous mutations haven’t happened yet.

    What the researchers did is pre-adapted it for mammals, and found once in them, it does adapt for airborne transmission (without any more directed mutations).

    If flu is incapable of evolving, is each new pandemic strain a design event?

  3. Semi OT:

    On this episode of ID the Future, Casey Luskin takes a keen-eyed look at Darwin’s tree of life and finds that common descent, far from being confirmed by the data, is actually contradicted by it, as New Scientist pointed out in a recent cover story, “Why Darwin was wrong about the tree of life.”
    http://intelligentdesign.podom.....7_20-07_00

  4. What are ‘neutral genomes’?

  5. DrREC:

    Or the variation the “organism must have” isn’t present and the organism goes extinct.

    Tell me, does the environment change in most locales from January to August? Do the species present in January somehow disappear in August?

    Do you see the speciousness of this line of reasoning?

    As to Dr. Liddle, I assure you, I have characterized her thinking quite closely.

  6. If flu is incapable of evolving, is each new pandemic strain a design event?

    You mean like the one we had two years ago?

    How often is there a real “pandemic”? The last, true “pandemic” was in 1918. Pandemics occur every, what, three hundred years? And in that time frame, how many replications of the flu have occurred? Huge amounts. So, yes, viruses can change over large periods of time; but, always withing certain limits—just as Dr. Behe has demonstrated in EoE.

  7. Ones that don’t have positive or negative charges.

  8. …but, seriously, why do you use the term ‘neutral genome’?

  9. I think he means genomes harboring neutral mutations?

    Which is hard to dispute the existence of.

    But then he goes on to ask about adaptive mutations in flu evolution.

    Puzzling.

  10. “Tell me, does the environment change in most locales from January to August? Do the species present in January somehow disappear in August?

    Do you see the speciousness of this line of reasoning?”

    I literally have no idea what this analogy is getting at.

    Your original post says:
    “Elizabeth Liddle is convinced that in any population there are neutral versions of the genome that have every needed variation an organism must have. Change the environment, and, lo and behold, the organism changes.”

    Which I point out is inane, because no scientist would say they MUST be equipped with these mutations, and the species could very well fail in the changed environment.

    “As to Dr. Liddle, I assure you, I have characterized her thinking quite closely.”

    I think not. Link?

  11. “You mean like the one we had two years ago?”

    The one that killed 18,200+ people?

    “How often is there a real “pandemic”? The last, true “pandemic” was in 1918. Pandemics occur every, what, three hundred years?”

    1968-1 Million dead
    1957-2 Million dead
    1918-50 million dead
    1890-1 million dead

    “, yes, viruses can change over large periods of time”

    Change? Due to evolution or design?

    The real power of this study is in showing that once adapted to mammals, that H5N1 quickly (in a small population of ferrets) developed mammal-to-mammal transmission with the evolution of two more mutations.

    This means that H5N1 infected mammals (pigs) should be culled, and humans monitored, so that these mutations cannot evolve.

    Of course, you put this past the edge of evolution, which makes this hypothesis the first ID prediction I can think of that would have dire consequences for human health if put into practice.

    Glad the CDC is staffed by evolutionary biologists.

  12. Thats just great. So scientists are trying to make strains of H5N1 more deadly. Are they ferret-hating monsters?

  13. DrREC:

    Change? Due to evolution or design?

    Design is not anti-evolution so what are you talking about?

  14. PaV is arguing there is an “edge of evolution,” beyond which there must have been design intervention,

    In natural flu, I want to know how many mutations/recombinations that is. 1? 3? 5?

  15. Dr REC:

    Obviously you don’t hold the same view as Elizabeth Liddle. But when I said, “In any population there are neutral versions of the genome that have every needed variation an organism must have. Change the environment, and, lo and behold, the organism changes,” I specifically had Elizabeth’s views in mind. You’ll remember I referenced her right off.

    You write:

    because no scientist would say they MUST be equipped with these mutations, and the species could very well fail in the changed environment.

    While I agree with you, I don’t think that Elizabeth really sees anything going extinct; or, if it does, this would be rare.

    So this post very much has her in mind. As to a link, just “google” her name, UD, and neutral drift, e.g.

  16. Dear DrREC:

    DrREC:The one that killed 18,200+ people?

    PaV:“How often is there a real “pandemic”? The last, true “pandemic” was in 1918. Pandemics occur every, what, three hundred years?”

    DrREC:
    1968-1 Million dead
    1957-2 Million dead
    1918-50 million dead
    1890-1 million dead

    The 18,200+ people was, what, about 18,000 below the normal flu outbreak?

    Hardly a “pandemic”.

    Look at your numbers: 50 million dead, given the population worldwide at the time is rather something, isn’t it? And this would constitute a “true pandemic”.

    That’s almost a hundred years ago. Shall we then go back to the bubonic plague, etc.?

    Change? Due to evolution or design?

    What has evolved? Do you mean has something changed? Yes, it has changed. This is the problem with putative “evolution”: it is an equivocal term, and misused because of this.

    Could it be “designed” this way? It’s possible. We don’t know enough right now to tell, one way or the other.

    The real power of this study is in showing that once adapted to mammals, that H5N1 quickly (in a small population of ferrets) developed mammal-to-mammal transmission with the evolution of two more mutations.

    Well, this is the “real power” of evolution. That’s all it can do, generally. In Behe’s EofE, he says that studies seem to indicate that it requires 10^20 replications of mutating genomes for a two amino acid change to take place. I’m sure, in the instance of this study, that is what took place in the virus genome.

    BUT, this is ALL evolution seems able to do. So, if you want to call this “power”, then go right ahead. But it sure seems enfeebled doesn’t it?

    I would invite you to read Behe’s Edge of Evolution.

    Of course, you put this past the edge of evolution, which makes this hypothesis the first ID prediction I can think of that would have dire consequences for human health if put into practice.

    Glad the CDC is staffed by evolutionary biologists.

    Maybe the problem is all of these evolutionary biologists?

    How are they spending our federal dollars? Do you remember all of the H5N1 vaccines that were produced? What a huge waste of money! But there were a host of pharmaceutical companies that did just fine with it.

    If these evolutionary biologists had read the EofE, maybe we wouldn’t have spent so much money? Weren’t they expecting it to mutate into something horrible? What happened?

    Now, over the course of a hundred years, or more, viruses could, simply because of the huge numbers of replications, change into highly virulent forms. But this takes large amounts of time. Certainly more than one year’s time.

    Frankly, when I heard all of the doom and gloom coming out of the CDC about H5N1, I reached for my wallet. But, of course, I’m not infected with Darwin-itis.

  17. DrREC:

    PaV is arguing there is an “edge of evolution,” beyond which there must have been design intervention,

    In natural flu, I want to know how many mutations/recombinations that is. 1? 3? 5?

    Generally two amino acids per 10^20 replications. More than that, appears to require intelligent input.

  18. paragwinn:

    I didn’t use the term “neutral genome”. I wrote: “neutral versions of the genome”.

    That is, genomes harboring many neutral (neither beneficial nor deleterious) mutations, as DrREC points out.

  19. DrREC:

    I think he means genomes harboring neutral mutations?

    Which is hard to dispute the existence of.

    But then he goes on to ask about adaptive mutations in flu evolution.

    Puzzling.

    I’ll first note that you wrote here: “adaptive mutations”. Aha! Adaptation; not evolution. We’re in agreement here.

    I’ve often stated, here at UD, that I’d agree with most of what Darwin had written if only he had titled his book: “Origin of Adaptations”.

    Now, to solve your puzzlement. If a.a.s are important, then they are conserved. If they’re not important, then they are neutral. Pretty much.

    Now, there might be ‘some’ mutations that are neutral generally, but afford some added fitness given a particular environment. So the genomes shuffle back and forth (generally). This is what is taken for “evolution”; which, as I just stated, is no more than “adaptation” for the most part.

    So, of course, I believe there are ‘neutral mutations’ present in viruses; but they’re likely of not much help (in killing people); yet, sometimes two a.a.s, changing at one time in one virus, can create quite a deadly virus. And “true pandemics” ensue.

    Hope that solves your puzzlement.

    But, again, there were two motivations for this post: (1) to counter Elizabeth Liddle’s sense that neutral mutations are always at the ready; and (2) to point out that Dr. Behe’s conclusion in EofE is once again confirmed.

    I think both have been demonstrated.

  20. PaV, here’s what I could find in her comments, and (unlike you) I will quote what she said:
    My point is that because neutral variants (currently neutral) can and do drift across the population, then a substantial pool of variants will tend to be maintained, even when none are currently advantageous or deleterious. This means that when a change in environment occurs, there is already a pool of potential variants that may prove advantageous in the new conditions – the population doesn’t have to wait for a brand new allele to come and rescue it in the nick of time!

    Nowhere that I can find does she suggest anything like “every needed variation an organism must have” is provided by neutral mutations. All she is saying is that neutral mutations can build up in a population and provide a pool of variants that are subject to natural selection when the environment changes. I completely agree with that. So why are you unwilling to provide us with the actual quote where she says that neutral mutations provide every needed variation that an organism need to survive environmental change. This is so clearly not the case, as Dr. REC has pointed out in the case of extinctions, that I can’t believe she made such a statement.

  21. NormO:

    Chew a little more on these words:

    This means that when a change in environment occurs, there is already a pool of potential variants that may prove advantageous in the new conditions – the population doesn’t have to wait for a brand new allele to come and rescue it in the nick of time

    You say:

    So why are you unwilling to provide us with the actual quote where she says that neutral mutations provide every needed variation that an organism need to survive environmental change.

    Can you see any difference between what you stated and Elizabeth Liddle’s quote? IOW, how are they any different?

  22. The term is in your OP title.
    Just because a genome harbors neutral muations does not make for a neutral version of a genome. Wouldnt the genome have to be made completely of neutral mutations (neutral in relation to making the harboring genome fit or unfit for environment) for there to be a ‘neutral version’ of the genome?

  23. one such exchange between Elizabeth and PaV is here:
    http://www.uncommondescent.com.....ra-fisher/

  24. PaV: “Elizabeth Liddle is convinced that in any population there are neutral versions of the genome that have every needed variation an organism must have.”

    DrRec: “In Elizabeth Liddle’s defense, I don’t think she would ever say such a thing. If I were you, I’d either link directly to her statement, or retract it promptly, with apologies.”

    Elizabeth Liddle (Quoted by NormO): “My point is that because neutral variants (currently neutral) can and do drift across the population, then a substantial pool of variants will tend to be maintained, even when none are currently advantageous or deleterious. This means that when a change in environment occurs, there is already a pool of potential variants that may prove advantageous in the new conditions – the population doesn’t have to wait for a brand new allele to come and rescue it in the nick of time!”

    DrRec and NormO are right. Elizabeth Liddle said there will be a POOL of varients that MAY prove advantageous, not that every population will have every needed varient. This makes sense and is in accord with observations

    You seriously misunderstood her and falsely accused her of saying something stupid and against observations. You owe Elisabeth Liddle an apology and a retraction.

    End of story. Apologize and retract. The longer you put it off, the worse you look.

  25. dmullenix:

    End of story. Apologize and retract. The longer you put it off, the worse you look.

    Yes, the worse I look in your eyes. I’m afraid this isn’t compelling motivation.

    Have you digested my response to NormO @ 1.1.1.1.2?

    Believe me, I’ve had my share of conversations with Elizabeth—who is a darling of sorts—but her views are really not tenable. That you think I’m badly misconstruing them is simply a hint at their untenable nature.

  26. You quote Dr. Liddle as saying “that may prove advantageous in the new conditions”, and then compare it to a quote of DrRec “neutral mutations provide every needed variation that an organism need to survive environmental change.” Then you say “Can you see any difference between what you stated and Elizabeth Liddle’s quote? IOW, how are they any different?”

    The difference is as plain as the difference between night and day. I’m puzzled that you can’t see it.

    Dr. Liddle is saying that there is a possibility that the population will have sufficient variants to get it through the problem. You are interpreting that as if it says the population will certainly have every possible variant.

    Possibility is not the same as certainty. Sufficient variants is not the same as every possible variant.

    My own view of evolution agrees with Dr. Liddle, but disagrees with what you seem to have taken her to be saying.

  27. How awesome that is for you.

    Once upon a time organisms evolved neutral alleles. The neutral alleles were not selected by natural selection, they just by random chance happened to exist. Like a computer program writing itself. And the program is useless. Until a magical thing happens. The environment changes and suddenly that useless program is just one or two digits away from becoming the killer app! Then natural selection occurs and *poof* that crazy neutral allele who’s parents said would never amount to anything is now the cause célèbre of the species!

    Of course this selection of neutral alleles only happens to lucky organisms when nobody is working. It’s called Science® my friends. It doesn’t have to be observable or repeatable.

  28. I) “While I agree with you, I don’t think that Elizabeth really sees anything going extinct; or, if it does, this would be rare.

    So this post very much has her in mind. As to a link, just “google” her name, UD, and neutral drift…”

    I did just that. I don’t find anything compelling to support your claim. I think you are engaging in defamation. No one believes extinction is rare. Again, provide a relevant quote from EL saying that nothing goes extinct, or retract this claim and apologize.

    II) “Generally two amino acids per 10^20 replications. More than that, appears to require intelligent input.”

    And how did Behe calculate this? Why would calculations applied to malaria or man apply to the flu virus, which has wholly different rates of recombination or mutation? Also note the assumption of methodological naturalism-that a ‘designer’ wasn’t reverting natural mutations, an assumption disposed with later.

    III) Do you see the circularity and non-falsifiability in your claims? You infer (from natural rates of mutation) that more than two changes in 10^20 replications, and that is designed. If I present something with more that number, that appears totally natural, then it is designed. Small, apparently natural=natural. Big apparently natural=designed.

    IV) Back to the original post, I don’t see how the evolution of influenza to become air-transmittable in a small experimental population of ferrets (once primed for mammalian infection with mutations already found in nature) disproves evolution. How many replications of virus passed through those ferrets?

    By the way, one reason this hasn’t emerged yet is the culling of mammals infected with avian flu. This article suggests we should keep up the vigilance.

  29. By the way, “neutral genomes” is still in the title.

    That term, I think, has only been used here.

  30. 30

    PaV:

    Have you digested my response to NormO @ 1.1.1.1.2?

    I’ve read 1.1.1.1.2, and I agree with dmullenix and Neil Rickert. Elizabeth said “there is already a pool of potential variants that may prove advantageous in the new conditions”; I don’t see any claim from her that any of the variants must be advantageous, and certainly not that the pool must include all needed variation. I have no idea how you could misread her that badly.

  31. Neil Rickert:

    It all depends on what the meaning of is is.

    The portion of Elizabeth Liddle’s quote you chose, i.e., “that may prove advantageous in the new conditions”, is followed by a dash. On the other side of the dash are these words: “the population doesn’t have to wait for a brand new allele to come and rescue it in the nick of time.”

    Now, I’m presuming you can both read and understand English. This being the case, you’ll notice that in saying an organism does not have to “wait for a brand new allele to come and rescue” the organism quite clearly means that it is already present within the organism. This is simple reading comprehension.

    I even bold-faced that portion of the quote. Why this willful mis-comprehension on yours and others part? Is it bias?

  32. Gordon:

    Please see 1.1.1.1.4 above.

    She doesn’t say they are “advantageous”; she says they become “advantageous” with changed conditions (the old Darwinian sleight-of-hand).

    Now, if the “pool” does NOT contain “all” needed variation, then it will die. I assume you agree with this. Then, obviously, the organism would not have to wait for the allele to show up. So, she is presuming that the organism survives. But, if the organism survives, then the “needed” variation was present in the “pool”. How else can you read it?

  33. No, the fact that you are misconstruing them is why they seem to you untenable :)

    And the idea that existing alleles that are neutral or even slightly deleterious in one environment may prove advantageous in a changed environment is not even controversial, is it? Everyone here accepts that “microevolution” occurs, and that’s exactly what “microevolution” is – what was a neutral size of beak in one year becomes an advantageous size of beak in the next.

    This isn’t “Darwinian sleight-of-hand” – it’s Darwin 101!

    But let me clarify a few terms: by “pool” I mean the “gene pool” of a population – the set of alleles extant in a given population at a given time. Not the set of alleles possessed by an individual.

    And what I am saying is really quite simple. In a sexually reproducing population (things are a little different for clones), there will be variants of every gene, known as alleles, and for many genes there will be many alleles. However, each individual only has a maximum of two alleles for each gene. Some alleles will be common in the population, and most organisms may possess both of them. Others will be rarer, and very few people will possess more than one. However, as long as there is plenty of genetic variety (lots of alleles) then when things change (weather, food supply) then that variance means that there will be some individuals who bear alleles that happen to be advantageous in the new conditions, and those alleles will become more common. And because new alleles are constantly being generated, as long as the population doesn’t get too small, there should always be a rich variety of alleles out of which the subset that do best in new conditions can be “selected” i.e. become more common.

    Does this make more sense? (It’s no different to what I’ve been saying, but I hope is less readily misunderstood.)

  34. On the contrary, extinction is very common. That’s one good reason to think that Shapiro is right about the evolution of evolvability – populations that manage to adapt and persist will tend to be those that with optimised mutation mechanisms, that ensure a steady feed of near-neutral mutations into the gene pool.

    Having said that, if habitats change too rapidly, and populations dwindle too fast, the gene pool itself will become impoverished, and a negative cycle of decline will tend to ensue, as we see happening in many habitats and populations right now.

  35. Looking at your title, PaV, I think there is some confusion. I said nothing about “neutral genomes” and I don’t know what such a thing would be at least in a sexually reproducing population. I have talked about neutral mutations, and neutral alleles, but in sexually reproducing populations, alleles can propagate independently from other alleles on the genome, so it doesn’t really make sense to talk about a “neutral genome” as the parental genotype is not passed in its entirety, no matter how fertile and healthy the parent.

  36. I think there’s been a miscommunication. If I used the phrase it would certainly have been a typo!

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